Worldwide, river fragmentation is primarily responsible for the decline of populations of migrating fish. In particular, anadromous fish species, which necessarily migrate to fresh water to reproduce, are endangered since many are no longer able to reach their natural spawning sites. In addition, pollution of rivers effectively prevents upstream or downstream movements and blocks access to spawning grounds. This article investigates how poor water quality interferes with the life history cycle of twaite shad Alosa fallax fallax (Lacépède, 1803), an anadromous clupeid fish, in the watershed of River Scheldt, a heavily impacted environment in West Europe. We used two models based on known ecological and environmental information to explain past and present twaite shad distribution within the watershed and to make inferences about a future population recovery and juvenile habitat value. We demonstrated that historical spawning areas satisfy water quality conditions necessary to support spawning and successful development of early life history stages of the twaite shad. However, poor water quality conditions just upstream the freshwater-saltwater boundary still act as an effective migration barrier for upstream movement. As a consequence, spawning grounds are inaccessible and the population is dominated by seasonal adults occurring in the lower estuarine part of the watershed. This article provides testable and diagnostic information to the watershed management in that it identifies habitat and water quality requirements needed to support the expected recovery of an endangered anadromous fish population.